Change version as this is not a patch release, but a minor one

build.gradle

@@ -12,7 +12,7 @@ buildscript {
 }
 apply plugin: 'net.minecraftforge.gradle.forge'
 
-version = "0.3.1"
+version = "0.4"
 group = "refinedstorage"
 archivesBaseName = "refinedstorage"
 

src/main/java/refinedstorage/RefinedStorage.java

@@ -19,7 +19,7 @@ import refinedstorage.proxy.CommonProxy;
 public final class RefinedStorage
 {
 	public static final String ID = "refinedstorage";
-	public static final String VERSION = "0.3.1";
+	public static final String VERSION = "0.4";
 
 	public static final SimpleNetworkWrapper NETWORK = NetworkRegistry.INSTANCE.newSimpleChannel(ID);
 

src/main/resources/mcmod.info

@@ -3,7 +3,7 @@
       "modid": "refinedstorage",
       "name": "Refined Storage",
       "description": "A Minecraft mod all about storage.",
-      "version": "0.3.1",
+      "version": "0.4",
       "mcversion": "1.9",
       "url": "",
       "updateUrl": "",